<tool id="reads_subsampler" name="Subsample FASTQ Reads" version="1.0.0" python_template_version="3.5">
    <description>to reduce excess genomic coverage</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $reads.reads_select == 'collection'
            python3 ${__tool_directory__}/subsamplr.py '$reads.coll.forward' '$reads.coll.reverse' '$downsampled.forward' '$downsampled.reverse' $coverage $genome_size '$seed'
        #else
            #if $reverse
                python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed'
            #else
                python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed'
            #end if
        #end if
    ]]></command>
    <inputs>
        <conditional name="reads">
            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
                <option value="collection">Paired collection from your history</option>
                <option value="history">Two FASTQ datasets from your history representing paired reads, forward and reverse</option>
                <option value="single">One FASTQ dataset representing single-end sequencing</option>
            </param>
            <when value="collection">
                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
            </when>
            <when value="history">
                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
            </when>
            <when value="single">
                <param label="Reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
            </when>
        </conditional>
        <param name="coverage" type="integer" label="Maximum Coverage" value="200" />
        <param name="genome_size" type="select" label="Assumed Genome Size">
            <option value="4500000">Salmonella, E. Coli (4500000)</option>
            <option value="2700000">Listeria (2700000)</option>
            <option value="29900">SARS-CoV-2 (29900)</option>
        </param>
        <param name="seed" type="text" value="ed2b99d842cddc1ac81d7c01a0bf0555" label="Random seed (you don't have to change this)"/>
    </inputs>
    <outputs>
        <data name="forward_out" label="${reads.forward.name}.downsampled" format_source="forward">
            <filter>reads['reads_select'] == "history" or reads['reads_select'] == "single"</filter>
        </data>
        <data name="reverse_out" label="${reads.reverse.name}.downsampled" format_source="reverse">
            <filter>reads['reads_select'] == "history"</filter>
        </data>
        <collection name="downsampled" type="paired" label="${reads.coll.name}" structured_like="reads|coll" format_source="reads|coll">
            <filter>reads['reads_select'] == "collection"</filter>
            <data name="forward" label="${reads.coll.forward.name}.downsampled" format_source="reads.coll.forward" />
            <data name="reverse" label="${reads.coll.reverse.name}.downsampled" format_source="reads.coll.reverse" />
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="reads">
                <param name="reads_select" value="collection" />
                <param name="coll">
                    <collection type="paired">
                        <element name="forward" value="forward.fastq" ftype="fastqsanger" />
                        <element name="reverse" value="reverse.fastq" ftype="fastqsanger" />
                    </collection>
                </param>
            </conditional>
            <param name="coverage" value="20" />
            <param name="genome_size" value="29900" />
            <output_collection name="downsampled" type="paired">
                <element name="forward" file="forward_out.fastq" />
                <element name="reverse" file="reverse_out.fastq" />
            </output_collection>
        </test>
        <test>
            <conditional name="reads">
                <param name="reads_select" value="history" />
                <param name="forward" value="forward.fastq" />
                <param name="reverse" value="reverse.fastq" />
            </conditional>
            <param name="coverage" value="20" />
            <param name="genome_size" value="29900" />
            <output name="forward_out" value="forward_out.fastq" />
            <output name="reverse_out" value="reverse_out.fastq" /> 
        </test>
        <test>
            <conditional name="reads">
                <param name="reads_select" value="history" />
                <param name="forward" value="forward.fastq.gz" />
                <param name="reverse" value="reverse.fastq.gz" />
            </conditional>
            <param name="coverage" value="20" />
            <param name="genome_size" value="29900" />
            <output name="forward_out" value="forward_out.fastq.gz"  decompress="true" />
            <output name="reverse_out" value="reverse_out.fastq.gz"  decompress="true" /> 
        </test>
        <test>
            <conditional name="reads">
                <param name="reads_select" value="history" />
                <param name="forward" value="forward.fastq.bz2" />
                <param name="reverse" value="reverse.fastq.bz2" />
            </conditional>
            <param name="coverage" value="20" />
            <param name="genome_size" value="29900" />
            <output name="forward_out" value="forward_out.fastq.bz2" decompress="true" />
            <output name="reverse_out" value="reverse_out.fastq.bz2" decompress="true" /> 
        </test>
    </tests>
    <help><![CDATA[
        Randomly subsample single or paired-end FASTQ reads to target a certain genomic coverage depth.
    ]]></help>
    <citations />
</tool>